OP0109 EXPRESSION QUANTITATIVE TRAIT LOCI IN EARLY TREATMENT-NAÏVE RHEUMATOID ARTHRITIS
Authors: K. Goldmann, E. Vigorito, C. Wallace, M. Barnes, A. Barton, C. Pitzalis, M. Lewis
Journal: Annals of the Rheumatic Diseases (2022)

Background To date more than 100 genetic loci have been associated with rheumatoid arthritis (RA), particularly in the human leukocyte antigen (HLA) region. Our understanding of the functional consequences of genetic variation in RA causality, however, is limited and it has been shown that a substantial portion of complex disease risk alleles modify gene expression in a cell-specific manner [1]. The Pathobiology of Early Arthritis Cohort (PEAC) is a longitudinal study looking at treatment-naiv̈e RA patients with genotyped data as well as both synovial and blood RNA-sequenced biopsies prior to treatment with disease modifying anti-rheumatic drugs (DMARDs). Objectives To explore expression quantitative trait loci (eQTL) in synovium and blood within PEAC and characterise the effects of genetic variation on gene expression measured by RNA-sequencing. A further goal was to investigate the role of these variants in RA disease severity and response variables. Methods Genotypes were generated by Illumina Human CoreExome-24 version 1-0 array in 118 RA patients. Single nucleotide polymorphisms (SNPs) in the HLA region were imputed using HLA-TAPAS. A candidate gene study was performed on variants within the HLA region using Plink v2.0. Synovial (n=85) and blood (n=51) RNA-sequenced samples then underwent cis -eQTL analysis (loci within ±5x10 5 Mb of the variant) based on linear regression models with the matrixeQTL R package using PEER [2] and PCA eigenvectors as covariates. Differences in eQTL between tissues were determined using a linear interaction term. Results The candidate gene study determined several amino acids around HLA-DRB1 acting as markers for seropositivity, which replicated findings by Raychaudhuri et. al. [3]. Using eQTL analysis, around 33,000 synovial SNPs were found with genome-wide significance (p ≤ 5x10 -8 ) and around 29,000 in blood. This corresponded to 279 unique significant genes in synovium and 417 in blood (Figure 1). There were 100 genes common to both synovium and blood, including PSORS1C3, HLA-DRB9 and ERAP2, which have known associations with autoimmune diseases and inflammatory arthritis. Notably, 92 genes showed significantly different patterns of QTL expression between synovial tissue and blood (p ≤ 5x10 -8 ). eQTL data also confirmed the triad of genetic variants significantly driving tissue gene expression of HLA-DPB2 , while both HLA-DPB2 SNPs and HLA-DPB2 RNA-sequencing synovial expression correlated highly with erythrocyte sedimentation rate (ESR). Figure 1. Manhattan plots for cis -expression quantitative trait loci (eQTL) analysis performed on 85 synovial samples (top) and 51 blood samples (middle). Tissue interaction eQTL (bottom) show significant differences between tissues (p ≤ 5x10 -8 ). Conclusion The high significance of genes in the HLA region in both tissues is in-keeping with the strong association between HLA and susceptibility to RA, as well as other autoimmune diseases. Most notably variants linked to HLA-DPB2 synovial expression were found to be a marker for disease severity through ESR association. Additionally, the significant differences between eQTL in blood and synovium highlight the need to explore functional consequences of genetic associations in the diseased tissue directly. References [1]Thalayasingam et. al. (2018). CD4+ and B lymphocyte expression quantitative traits at rheumatoid arthritis risk loci in patients with untreated early arthritis: implications for causal gene identification. Arthritis &amp; Rheumatology, 70(3), 361-370. [2]Stegle et al. (2012). Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses. Nature protocols, 7(3), 500-507. [3]Raychaudhuri et al. (2012). Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis. Nature genetics, 44(3), 291-296. Disclosure of Interests None declared